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gnu: bioinformatics: Return #t from all phases and snippets.

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* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk)
(codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish)
(salmon): Return #t from all phases and snippets, use 'invoke' where
appropriate, and remove vestigal plumbing.
This commit is contained in:
Mark H Weaver 2018-06-27 19:52:54 -04:00
parent 96272e2822
commit 2e0f69057a
No known key found for this signature in database
GPG key ID: 7CEF29847562C516
1 changed files with 31 additions and 16 deletions
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47
gnu/packages/bioinformatics.scm
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@ -281,7 +281,8 @@ (define-public bamtools
(setenv "LDFLAGS"
(string-append
"-Wl,-rpath="
(assoc-ref outputs "out") "/lib/bamtools")))))))
(assoc-ref outputs "out") "/lib/bamtools"))
#t)))))
(inputs `(("zlib" ,zlib)))
(home-page "https://github.com/pezmaster31/bamtools")
(synopsis "C++ API and command-line toolkit for working with BAM data")
@ -496,7 +497,8 @@ (define-public ribotaper
'("create_annotations_files.bash"
"create_metaplots.bash"
"Ribotaper_ORF_find.sh"
"Ribotaper.sh"))))))))
"Ribotaper.sh")))
#t)))))
(inputs
`(("bedtools" ,bedtools-2.18)
("samtools" ,samtools-0.1)
@ -591,7 +593,8 @@ (define-public bioawk
(man (string-append out "/share/man/man1")))
(mkdir-p man)
(copy-file "awk.1" (string-append man "/bioawk.1"))
(install-file "bioawk" bin)))))))
(install-file "bioawk" bin))
#t)))))
(home-page "https://github.com/lh3/bioawk")
(synopsis "AWK with bioinformatics extensions")
(description "Bioawk is an extension to Brian Kernighan's awk, adding the
@ -1811,7 +1814,8 @@ (define-public codingquarry
(copy-recursively "QuarryFiles"
(string-append out "/QuarryFiles"))
(install-file "CodingQuarry" bin)
(install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
(install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))
#t)))))
(inputs `(("openmpi" ,openmpi)))
(native-search-paths
(list (search-path-specification
@ -2727,7 +2731,8 @@ (define-public fraggenescan
(share (string-append out "/share/fraggenescan/train")))
(install-file "run_FragGeneScan.pl" bin)
(install-file "FragGeneScan" bin)
(copy-recursively "train" share))))
(copy-recursively "train" share))
#t))
(delete 'check)
(add-after 'install 'post-install-check
;; In lieu of 'make check', run one of the examples and check the
@ -4153,7 +4158,8 @@ (define-public minced
"#!" (assoc-ref inputs "bash") "/bin/sh\n\n"
(assoc-ref inputs "jre") "/bin/java -jar "
bin "/minced.jar \"$@\"\n"))))
(chmod wrapper #o555)))))))
(chmod wrapper #o555))
#t)))))
(native-inputs
`(("jdk" ,icedtea "jdk")))
(inputs
@ -4408,7 +4414,7 @@ (define pplacer-scripts
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-scripts-dir
(lambda _ (chdir "scripts")))
(lambda _ (chdir "scripts") #t))
(replace 'check
(lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
(add-after 'install 'wrap-executables
@ -6019,7 +6025,8 @@ (define-public star
(lambda _
(substitute* "Makefile"
(("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
(string-append pre "Built with Guix" post)))))
(string-append pre "Built with Guix" post)))
#t))
(add-after 'enter-source-dir 'do-not-use-bundled-htslib
(lambda _
(substitute* "Makefile"
@ -6103,7 +6110,8 @@ (define-public subread
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(mkdir-p bin)
(copy-recursively "../bin" bin))))
(copy-recursively "../bin" bin))
#t))
;; no "configure" script
(delete 'configure))))
(inputs `(("zlib" ,zlib)))
@ -12006,11 +12014,13 @@ (define-public sailfish
(add-after 'unpack 'do-not-look-for-boost
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
(("find_package\\(Boost 1\\.53\\.0") "#"))))
(("find_package\\(Boost 1\\.53\\.0") "#"))
#t))
(add-after 'unpack 'do-not-assign-to-macro
(lambda _
(substitute* "include/spdlog/details/format.cc"
(("const unsigned CHAR_WIDTH = 1;") ""))))
(("const unsigned CHAR_WIDTH = 1;") ""))
#t))
(add-after 'unpack 'prepare-rapmap
(lambda* (#:key inputs #:allow-other-keys)
(let ((src "external/install/src/rapmap/")
@ -12026,7 +12036,8 @@ (define-public sailfish
(for-each (lambda (file)
(install-file file src))
(find-files "/tmp/rapmap/src" "\\.(c|cpp)"))
(copy-recursively "/tmp/rapmap/include" include))))
(copy-recursively "/tmp/rapmap/include" include))
#t))
(add-after 'unpack 'use-system-libraries
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("src/SailfishIndexer.cpp"
@ -12066,7 +12077,8 @@ (define-public sailfish
(string-append (getenv "CPLUS_INCLUDE_PATH")
":"
(assoc-ref inputs "eigen")
"/include/eigen3")))))))
"/include/eigen3"))
#t)))))
(inputs
`(("boost" ,boost)
("eigen" ,eigen)
@ -12252,11 +12264,13 @@ (define-public salmon
(add-after 'unpack 'do-not-look-for-boost
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
(("find_package\\(Boost 1\\.53\\.0") "#"))))
(("find_package\\(Boost 1\\.53\\.0") "#"))
#t))
(add-after 'unpack 'do-not-phone-home
(lambda _
(substitute* "src/Salmon.cpp"
(("getVersionMessage\\(\\)") "\"\""))))
(("getVersionMessage\\(\\)") "\"\""))
#t))
(add-after 'unpack 'prepare-rapmap
(lambda* (#:key inputs #:allow-other-keys)
(let ((src "external/install/src/rapmap/")
@ -12273,7 +12287,8 @@ (define-public salmon
"external/install/include/rapmap/concurrentqueue.h"
"external/install/include/rapmap/FastxParserThreadUtils.hpp"
"external/install/src/rapmap/FastxParser.cpp"
"external/install/src/rapmap/xxhash.c")))))
"external/install/src/rapmap/xxhash.c")))
#t))
(add-after 'unpack 'use-system-libraries
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/CMakeLists.txt"